fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
logspace.hpp
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1// --------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
4// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
6// --------------------------------------------------------------------------------------------------
7
8#pragma once
9
10#include <cmath>
11
13{
14
15constexpr double ln_2{0.693147180559945309417232121458176568L};
16constexpr double negative_inf{-std::numeric_limits<double>::infinity()};
17
19// Produces correct result if either term is -inf.
20// Needs a check for the case where both terms are -inf.
21[[nodiscard]] inline double add(double const log_x, double const log_y) noexcept
22{
23 double const max{std::max(log_x, log_y)};
24 return max == negative_inf ? negative_inf : max + std::log1p(std::exp(-std::abs(log_x - log_y)));
25}
26
28template <typename... types>
29[[nodiscard]] double add(double const log_x, double const log_y, types... logs) noexcept
30{
31 return add(add(log_y, log_x), logs...);
32}
33
35// expm1 is more accurate than using exp if the difference is close to 0.
36[[nodiscard]] inline double substract(double const log_x, double const log_y) noexcept
37{
38 double const difference{log_y - log_x};
39 return log_x + difference > -ln_2 ? std::log(std::expm1(difference)) : std::log1p(-std::exp(difference));
40}
41
42struct add_fn
43{
44 [[nodiscard]] double operator()(double const log_x, double const log_y) const noexcept
45 {
46 return add(log_x, log_y);
47 };
48};
49
50} // namespace raptor::logspace
Definition: logspace.hpp:13
double substract(double const log_x, double const log_y) noexcept
The log of a difference of two log terms. (log_x - log_y)
Definition: logspace.hpp:36
double add(double const log_x, double const log_y) noexcept
The log of a sum of two log terms.
Definition: logspace.hpp:21
constexpr double negative_inf
Definition: logspace.hpp:16
constexpr double ln_2
Definition: logspace.hpp:15
Definition: logspace.hpp:43
double operator()(double const log_x, double const log_y) const noexcept
Definition: logspace.hpp:44